Rather than answer this in the Revan vs. Nihilus thread, I think this deserves its own thread, since I have not discussed this here or seen similar theories before.

Anyway, the main gist of my theory on Nihilus' origin goes is based in the idea that the exile is connected to Nihilus and, if my theory is correct, actually IS Nihilus. This all boils do to what exactly happened to the exile during the battle of Malachor V, when he cut his own connection to the force.

As both HK-47 (of all people) and Kreia explain during TSL, Darth Revan used the Mandalorian Wars to subvert the jedi and turn them to the dark side. By doing so he forced a choice, since the final battle was something nobody could walk away from - the jedi could either turn to the dark side or they could die, no exceptions. Save one.

The exile, and the exile alone, avoided both of these options, but only by embracing a third, that is perhaps even more terrible. The exile did not want to die, but he also denied the will of the force, which dictated that he MUST fall to the dark side, if he were to live. But the exile refused that fate so severely, that he cut all his ties to the force and left a wound behind in the the force itself.

Yet as Zez-Kai Ell tells us, such a wound does not simply go away. It remains behind, although it is empty. It is this empty that is Nihilus, IMHO. He is the dark side or dark self of the proto-exile, that the exile rejected at Malachor V. The exile has no force powers of his own - he only has access to the force through his connections with others - because Nihilus IS the very force connection that he rejected so long ago.

Nihilus is both like a rejected splinter of the exile's soul, but it is probably easier to explain it, if we compare him to an arm infected with gangrene. This infection is terminal, and in order save himself from it, the exile cuts off his "arm." In doing so, however, he shed the part of himself that had already fallen to that dark side.

This evil self "survived" by claiming the dead or near-dead body of a fallen jedi and then became Darth Nihilus (a friend or old master of the Exile would make the most sense, since the connection would be stronger). Note how Nihilus and the Exile share the ability to resist the will of the force and gain strength by draining or siphoning it from others, though that ability is said to be unique. By resisting the will of the force, the Exile simply split him/herself in two in spite of the actions that had been taken on Malachor. You might not call the Exile light side (as opposed to Nihilus being obviously dark sided), yet note how the jedi masters say that the Exile was the only jedi to ever return to face their judgment after leaving for the Mandalorian Wars. According to Revan's plans, the Exile should never have been able to do this (as per HK-47's comments about Revan 'cleaning house" on Malachor V), and yet the Exile resisted this fate.

So the Exile is not whole, which explains the wound in the force and the need to rely on force bonds to other in order to gain access to the force. The Exile's fate was to turn to the dark side, and therefore the force powers have remained with the side that became Nihilus.

Now, before you object, there are a few things you should consider, since I based this theory on just on my own wild ideas, but from clues and comments in TSL that seemed unexplained or inconclusive to me. While I like think that I'm not so arrogant as to presume that this is indeed the officially planned origin-story of Nihilus, this means that there are details to support it. These include:

The Exile is specifically connected to Nihilus because he was the only jedi to resist the corruption and perversion of the jedi that Revan staged on Malachor V:

HK-47: "That is why Revan felt that Malachor V was so important. It was intended to be a conversion tool. Assessment: When faced with a continuous series of hard-fought battles, I detected a significant statistical increase in Jedi following Revan over the Jedi Code - a compromise in principles brought about by battlefield conditions.The emotional weight of war changed Jedi morale, power, and eventually, their allegiance. Conclusion: I believe the Mandalorian Wars were to beat the Mandalorians and also to allow Revan to build the foundation of his army. But I am surprised you have not already arrived at this conclusion. Surely the loss of your troops and the Jedi who served under you at Malachor V, had a detrimental effect upon you and your ties to the Force - and I suspect, your desire to be around others ever again."

This establishes my point above about how no jedi (but the exile) could escape the choice Revan put before them: Fall to the dark side or die! That the exile did make a third choice makes him unique. No other jedi could avoid this choice, and here is the reason:

HK-47: "Observation: Master, that was the lesson of Malachor. Any Jedi involved in the systematic slaughter on such a scale cannot help but doubt and question themselves.Observation: Master, I do not believe that the Mandalorians were the true target at Malachor - I believe that the intention was to destroy the Jedi, break their will, and make them loyal to Revan.I do not know if you examined the records of the deaths on Malachor, but you cannot escape that many of the Jedi and Republic soldiers who died were not Revan's strongest supporters. Observation: I believe that Revan was "cleaning house" at Malachor V. What ones did not die became Revan's allies against the Republic."

The last bit here is particularly important, because it underscores the exile's unique situation. Kreia says it even better to the comatose LS exile after the meeting with the masters on Dantooine:

Kreia: "There is a place in the galaxy where the dark side of the Force runs strong. It is something of the Sith, but it was fueled by war. It corrupts all that walks on its surface, drowns them in the power of the dark side - it corrupts all life. And it feeds on death. Revan knew the power of such places... and the power in making them. They can be used to break the will of others... of Jedi, promising them power, and turning them to the dark side.Did you never wonder how Revan corrupted so many of the Jedi, so much of the Republic, so quickly?The Mandalorian Wars were a series of massacres that masked another war, a war of conversion.Culminating a final atrocity that no Jedi could walk away from... save one.And that is what I sought to understand. How one could turn away from such power, give up the Force... and still live. But I see what happened now. It is because you had no choice.It is because you were afraid."

These comments contain some revelation. Clearly the place she talks about is Malachor V, and we learn that only the Exile was able to turn away from it. Kreia has been trying to find out how that was possible, and now has discovered that it was due to fear. That fear fits rather well with the neurosis theory of what happened to separate the Exile and Nihilus - the Exile sensed a darkness within and fled from it by subconsciously cutting himself off from the Force. In that sense, this fear is what gave birth to Nihilus, and as a Yoda would tell us, fear leads to the dark side. Zez-Kai Ell also underscores the importance of force bonds. He is talking about the exile's bond with Kreia, but given that the exile has a connection to Nihilus (and I will establish that below), his comments are just as relevant - if not more so - to the connection with Nihilus.

Zez-Kai Ell: "such bonds are a connection that can be formed at moments of crisis - or in the slow understanding that grows between master and apprentice.It is most common between two beings who are sensitive to the Force. It allows the transmission of feelings, of influence. {Musing}It was something you were gifted with, as I recall, before your fall. You formed such attachments easier than most - even to those who could feel the Force only faintly. {Rueful}Even Vrook could not ignore it, which is saying something. {Frowns}That is most unusual - and unnatural. I have never heard of a bond of such strength. There were a few within the Order who knew more than I did of such bonds - but their students were few, lost in the Mandalorian Wars. It was rumored that Revan studied such bonding deeply, both through the Jedi histories and with certain teachers, before he left the Order and went to war. It was rumored that Revan studied such bonding deeply, both through the Jedi histories and with certain teachers, before he left the Order and went to war. I do not know - a bond between two living beings is not something easily broken. It not a choice... it is like breaking a feeling. Like turning away from the Force.To break a bond, your feelings would have to change, or one of you would have to die - but even then, the bond wouldn't go away, it would simply... it would simply be empty, a wound.{Becomes quieter at the end}One of you would have to die, but even then, the bond wouldn't go away, it would simply... it would simply be empty, a wound."

Kreia also notes what happened on Malachor V to turn the jedi who fought there to the dark side:

Kreia: "Many believed the Mandalorians defeated at Malachor V. But the Mandalorians taught the Jedi much through battle. And so it was that Malak, Revan, and the Jedi that followed them discovered their true natures in the Mandalorian crusade."

In the cut content of KotOR2, jedi master Vash has some comments on force wounds that are extremely interesting in the Exile/Nihilus context:

Vash: "Look within for the answer. We are each solely accountable for everything in our lives. Nothing ever happens to us unless we allow it."

This was cut, but it was intended to be in the game.

Now, I said I would establish the connection between exile and Nihilus, and it is actually simple, since the masters tell us. They don't mention Nihilus by name, since they don't know exactly what happened, but given that we know Nihilus was behind the devastation of Katarr, there is little or - in fact- no doubt at all.

Just note what the masters tell the Exile when they meet on Dantooine in KotOR2:

"The last Jedi conclave was on Katarr, a Miraluka colony. And all of Katarr was destroyed, all of the Jedi killed...Including Master Zhar... Master Vandar... A Jedi doesn't care if he dies. Everyone does, but when we fight, when we sacrifice ourselves, it is for others, for the greater good. But our presence must not endanger others. And as long as we were visible targets, we were a threat to everything around us.There was a gathering of Jedi on the planet - when we realized that something was attacking us, we resolved to meet secretly to attempt to find this threat.Then... Katarr was no more.When we felt Katarr die, there is something we felt, something we'd felt once before. An echo in the Force.We'd felt it before when you stood before us. Whatever this threat, whatever this hunger is, it is something tied to you, something you have experienced directly. This echo travels in the places where death has walked, where planets have died. Massacres fuel its power, the death of life fuels it."

Here the connection between Nihilus and the Exile becomes very clear - the masters felt the same echo in Nihilus that they had felt from the Exile years before when they exiled him. Of course, it might then be argued that this is merely a reference to the horrors of Malachor V that spawned both Nihilus and made the Exile what he has become. However, another part of the masters meeting suggests otherwise:

"The Sith are a threat, it is true. But the threat they present... it is tied to you in some way. The echo we have felt on the worlds we have walked - we have encountered it only once before, when you stood before us at your trial.We believe that somehow, you are creating this - or that the Sith have learned this technique from you."

Here is it undeniable that the Exile is directly tied to the threat the Sith represent, and since the connection is tied to the "echo" they have felt from both the Exile (when he was exiled) and Nihilus (when Katarr was destroyed), it cannot be simply due to their mutual ties to Malachor V - others were there on Malachor V (Sion and Kreia, for example, and the all the jedi who followed Revan and Malak), and yet they carry none of these echoes or powers.

"It is all that is left unsaid upon which tragedies are built" - Kreia